Wednesday, October 31, 2007

Oct 2007 Dagstuhl Seminar Invitation

I have been invited to attend a Dagstuhl Seminar in May of 2008 on Graph Drawing with Applications to Bioinformatics and Social Sciences. This is a very timely event for me, as I am working with a number of grad students, namely Mike Bennett, Mike Farrugia and Eamon Phelan on just these two areas. In addition Brendan Sheehan MSc, one of my grad students, has been developing the research and method behind CellTransformer: A Tool to Generate Reaction Networks through Graph Transformation. The timing is a little tight as I need to fly to Australia shortly afterwards where I'm the Late Breaking Results Co-Chair for Pervasive 2008, the Sixth International Conference on Pervasive Computing.

I'm looking forward to hearing about work in both Bioinformatics and the Social Sciences and any new techniques and applications that are emerging.

To quote to organisers!

"Automated graph drawing deals with the layout of relational data arising from computer science (data base design, data mining, software engineering), and other sciences such as bioinformatics (metabolic networks, protein-protein interaction), business informatics (business process models), and criminalistics (social networks, phone-call graphs). In mathematical terms, such relational data are modeled as graphs or more general structures such as hypergraphs, clustered graphs, or compound graphs. Graph drawing communicates the relational information through diagrams drawn in the plane. The main objective is to display the data in a meaningful fashion, that is, in a way that shows well the underlying structures, and that often depends on the application domain.

In this seminar, we will to focus on graph drawing in two important application domains: bioinformatics (metabolic pathways, regulatory networks, protein-protein interaction) and social sciences and criminalistics (case information diagrams, phone-call graphs). In both application domains, the underlying information is usually stored in large data bases constituting a huge and complex graph, but only a suitable fraction of this graph is visualized and the exploration of the underlying graph is guided by the user. Thus, the user becomes a central actor that triggers dynamic updates of the displayed graph and its layout. The support of application-specific update functionality in conjunction with high quality graph layout is essential in order to gain user acceptance in the targeted application areas."

Friday, October 19, 2007

Oct 2007 Three Open Postdoc Posts

3 postdoctoral research positions available in:

* wireless sensor networks
* software engineering for autonomic systems
* enterprise systems engineering

Systems Research Group
School of Computer Science and Informatics
UCD Dublin, Belfield, Dublin 4, Ireland

The group

UCD's Systems Research Group conducts world-recognised research in
software and systems engineering, with particular emphasis on
pervasive computing, autonomic communications, software development of
dependable systems, complex systems visualisation and embedded systems
design. SRG is unique in spanning the range of systems disciplines
from hardware and programming up to mathematical modeling and
analysis, and places great emphasis on collaborative research that
leverages this expertise. The group is accommodated within UCD's
Complex and Adaptive Systems Laboratory (CASL,, a
groundbraking facility that brings together researchers in computer
science, mathematics, bioinformatics, physical and earth sciences to
conduct researech in a highly cross-disciplinary environment. SRG
currently consists of five academic staff, three postdoctoral
researchers and around 30 graduate students (almost all fully-funded)
studying both full- and part-time for advanced degrees. The group has
a current grant portfolio worth over EUR3.5M and a publication output
of over 30 papers per year in world-leading conferences and journals.

As part of its on-going research programme, SRG has vacancies for
three talented and well-motivated postdoctoral researchers to help
drive the group's evolution. Suitable candidates will have a
successful academic record to doctoral level, together with a
portfolio of internationally peer-reviewed conference and journal
publications and evidence of significant future potential in
research. Furthermore they will be expected to engage broadly in the
development of the group, the supervision of graduate students and
other activities.

Salaries for all three posts will be in the range EUR37,886 -
EUR46,043 depending on qualifications and experience. All posts are of
two years' durattion with the possibility of extension, and will be
probational for the first 12 months.

The positions

Postdoctoral researcher in wireless sensor networks

The successful candidate will conduct and manage research in the area
of wireless sensor networks embedded into the built environment,
providing advanced sensor and actuator capabilities within built
artefacts. This will take place within the framework of a large-scale
collaboration managed by Cork Institute of Technology and including
several other Irish universities and public bodies, which will also
fund two studentships in the area. A track record of research in one
or more of pervasive computing, network analysis, embedded systems
development and systems architecture are essential, as is a
willingness to learn and work in a variety of new areas. Further
particulars can be obtained from Dr Simon Dobson

Postdoctoral researcher in software engineering for autonomic systems

The successful candidate will work in conjunction with LERO, the Irish
Software Engineering Research Centre ( to conduct
research into improving the principles and practice of engineering
autonomic systems -- self-managing, self-optimising, self-healing and
so forth. Current interests include programming languages and
approaches, middleware, complex systems visualisation, and
mathematical models of software engineering, and a track record in one
or more of these areas are essential. The researcher will join a team
including an exisiting postdoc and four fully-funded graduate
students. Further particulars can be obtained from Dr Aaron Quigley

Postdoctoral researcher in enterprise systems engineering

The successful candidate will work in collaboration with Oracle
Ireland Ltd on the development of improved models and techniques for
diagnosing, predicting and managing faults and failures within
large-scale distributed software systems. A track record in one or
more of distributed systems, autonomic computing, dependable systems,
fault-tolerance and fault analysis are essential. Further particulars
may be obtained from Prof Paddy Nixon (

To apply

Please direct expressions of interest (including short CV) to the
contact individual named above for the specific post of
interest. Applications will be accepted until all posts are filled.


Sunday, October 14, 2007

Oct 2007 European Patent Office Invention Filed

As part of my role as an IBM CAS Visiting Scientist I work with Extreme Blue groups during the summer period. Three of my former UCD honours student Keith, Cheryl and Darin have ended up on Extreme Blue. I consider it to be an exceptional opportunity for any grad to understand and experience industrial R&D. My involvement with Extreme Blue is a collaboration and often results in invention disclosures and from time to time a patent is filed. One such patent for a mobile recommendation invention was recently filed in Europe and we expect a follow up international application in the months to come.

Friday, October 12, 2007

Oct 2007 Tom Holland starts as IRCSET funded postgrad

I would like to welcome Tom Holland who recently started his Ph.D. with the Systems Research Group in the UCD Complex and Adaptive Systems Laboratory under my supervision with Prof. Paddy Nixon. Tom is starting his research in the area of richly sensorised pervasive computing environments. Tom has received a full scholarship from the Irish Research Council for Science, Engineering and Technology (IRCSET). He is already busy at work on the course work component of his structured PhD program, a small Ubisense location project and we have had initial contacts with an industrial partner for collaboration on his research. Tom completed his B.Sc. in Internet Computing at the University of Hull in 2006 and previously spent 3 years in commercial development roles with digital agencies in Newcastle Upon Tyne and most recently with Acknowledgement Ltd. in London. Welcome to the SRG Tom and your first paper deadline is April for UbiComp 2008!

Monday, October 01, 2007

Sept 2007 CellTransformer: A Tool to Generate Reaction Networks through Graph Transformation

Brendan Sheehan MSc, one of the PhD scholars I supervise is off to The Eighth International Conference on Systems Biology, Long Beach California Oct 1-6, 2007. He is attending various tutorials and presenting a poster on his research, namely: "CellTransformer: A Tool to Generate Reaction Networks through Graph Transformation"

ICSB 2007

Rule-based models provide a declarative means to construct a computational model of biological systems. Rules specify how the model can evolve over time by transforming the underlying data or model into its next state. Most rule-based systems operate on strings. Graph transformation systems (GTS) can provide a more direct and intuitive description of many kinds of biological data such as protein-interaction data and data relating to cell-signalling pathways. Here we implement the GTS based formalism defined by Blinov et al to help generate molecular reactions based on rules that describe interactions between protein domains. We use the GTS tool AGG to implement the tool as a plugin for the forthcoming version of CellDesigner.
by Sheehan and Quigley.